library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(viridis)
## Loading required package: viridisLite
# Load the knitr package if not already loaded
library(knitr)
# Source the R Markdown file
knit("/Users/bailey/Documents/research/fish_biodiversity/src/collection/load_collection_data.Rmd", output = "/Users/bailey/Documents/research/fish_biodiversity/src/collection/load_collection_data.md")
##
##
## processing file: /Users/bailey/Documents/research/fish_biodiversity/src/collection/load_collection_data.Rmd
##
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## output file: /Users/bailey/Documents/research/fish_biodiversity/src/collection/load_collection_data.md
## [1] "/Users/bailey/Documents/research/fish_biodiversity/src/collection/load_collection_data.md"
Stratification_at_props_BodyShape <- Stratification_at %>%
group_by(Strat, BodyShapeI) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
BodyShape_plot_weighted <- ggplot(Stratification_at_props_BodyShape, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = BodyShapeI)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = BodyShapeI), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Body Shape", values = c(11, 21:25), labels = c("1o" = "other", "2s" = "short deep", "3f" = "fusiform", "4e" = "elongated", "5l" = "eel-like")) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,0.6)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "A")
BodyShape_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/BodyShape_plot_weighted.png", BodyShape_plot_weighted, width = 6, height = 4, units = "in")
# BodyShape_plot_weighted <- ggplot(Stratification_at_props_BodyShape, aes(fill=Stratification, y=proportion, x=BodyShapeI)) +
# geom_bar(position='dodge', stStratification_at='identity') +
# scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
# guides(fill = "none", color = "none") +
# theme_bw() +
# theme(text = element_text(size = 24),
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Body Shape")
# BodyShape_plot_weighted
# ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/BodyShape_plot_weightedbar.png", BodyShape_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# BodyShape_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$BodyShapeI)
#
# # Divide each count by the total number of rows to find the proportion
# BodyShape_props <- BodyShape_counts/(rowSums(BodyShape_counts))
# BodyShape_props
#
# BodyShape_props <- as.dStratification_ata.frame(BodyShape_props)
#
# BodyShape_props$Var1 <- factor(BodyShape_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# BodyShape_plot <- ggplot(BodyShape_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("BodyShape")
# BodyShape_plot
DemersPelag
Stratification_at_props_DemersPelag <- Stratification_at %>%
group_by(Strat, DemersPelag) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
DemersPelag_plot_weighted <- ggplot(Stratification_at_props_DemersPelag, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = DemersPelag)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = DemersPelag), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Demersal Pelagic", values = c(21:25, 12:13),
labels = c("1r" = "reef-associated", "2pn" = "pelagic-neritic", "3p" = "pelagic", "4po" = "pelagic-oceanic", "5d" = "demersal", '6bp' = 'benthopelagic', '7bd' = 'bathydemersal')) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,1)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification")
DemersPelag_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/DemersPelag_plot_weighted.png", DemersPelag_plot_weighted, width = 6, height = 4, units = "in")
Stratification_at_props_OperculumPresent <- Stratification_at %>%
group_by(Strat, OperculumPresent) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
OperculumPresent_plot_weighted <- ggplot(Stratification_at_props_OperculumPresent, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = OperculumPresent)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = OperculumPresent), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Operculum", values = c(21:22)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,0.75)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "B")
OperculumPresent_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/OperculumPresent_plot_weighted.png", OperculumPresent_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# OperculumPresent_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$OperculumPresent)
#
# # Divide each count by the total number of rows to find the proportion
# OperculumPresent_props <- OperculumPresent_counts/(rowSums(OperculumPresent_counts))
# OperculumPresent_props
#
# OperculumPresent_props <- as.dStratification_ata.frame(OperculumPresent_props)
#
# OperculumPresent_props$Var1 <- factor(OperculumPresent_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# OperculumPresent_plot <- ggplot(OperculumPresent_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("OperculumPresent")
# OperculumPresent_plot
DorsalSpinesMean_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= DorsalSpinesMean, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylab("Dorsal Spines") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "C")
DorsalSpinesMean_plot_weighted
## Warning: Removed 10 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 10 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 10 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 10 rows containing missing values (`geom_point()`).
# Twelve values with NA
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/DorsalSpinesMean_plot_weighted.png", DorsalSpinesMean_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 10 rows containing non-finite values (`stat_ydensity()`).
## Removed 10 rows containing missing values (`geom_point()`).
# DorsalSpinesMax_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= DorsalSpinesMax, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("DorsalSpinesMax")
# DorsalSpinesMax_plot
MaxLengthTL_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= MaxLengthTL, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,450)) +
ylab("Length (cm)") +
xlab("Stratification") +
labs(colour = "Stratification")
MaxLengthTL_plot_weighted
## Warning: Removed 3 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 3 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 3 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 3 rows containing missing values (`geom_point()`).
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/MaxLengthTL_plot_weighted.png", MaxLengthTL_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 3 rows containing non-finite values (`stat_ydensity()`).
## Removed 3 rows containing missing values (`geom_point()`).
# MaxLengthTL_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= MaxLengthTL, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("MaxLengthTL")
# MaxLengthTL_plot
Troph_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= Troph, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylab("Trophic Level") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "D")
Troph_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/Troph_plot_weighted.png", Troph_plot_weighted, width = 6, height = 4, units = "in")
# Troph_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= Troph, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Troph")
# Troph_plot
DepthMin_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= DepthMin, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(-1,201)) +
ylab("Depth Min (m)") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "A")
DepthMin_plot_weighted
## Warning: Removed 8 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 8 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 8 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 8 rows containing missing values (`geom_point()`).
# One value with NA
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/DepthMin_plot_weighted.png", DepthMin_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 8 rows containing non-finite values (`stat_ydensity()`).
## Removed 8 rows containing missing values (`geom_point()`).
# DepthMin_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= DepthMin, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("DepthMin")
# DepthMin_plot
DepthMax_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= DepthMax, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(-1,1001)) +
ylab("Depth Max (m)") +
xlab("Stratification") +
labs(colour = "Stratification")
DepthMax_plot_weighted
## Warning: Removed 10 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 10 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 10 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 10 rows containing missing values (`geom_point()`).
# One value with NA
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/DepthMax_plot_weighted.png", DepthMax_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 10 rows containing non-finite values (`stat_ydensity()`).
## Removed 10 rows containing missing values (`geom_point()`).
# DepthMax_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= DepthMax, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("DepthMax")
# DepthMax_plot
TempPrefMin_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= TempPrefMin, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylab("Temp Min (Cº)") +
xlab("Stratification") +
labs(colour = "Stratification")
TempPrefMin_plot_weighted
## Warning: Removed 9 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 9 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 9 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 9 rows containing missing values (`geom_point()`).
# Two values with NA
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/TempPrefMin_plot_weighted.png", TempPrefMin_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 9 rows containing non-finite values (`stat_ydensity()`).
## Removed 9 rows containing missing values (`geom_point()`).
# TempPrefMin_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= TempPrefMin, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("TempPrefMin")
# TempPrefMin_plot
TempPrefMax_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= TempPrefMax, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(17.5,30)) +
ylab("Temp Max (Cº)") +
xlab("Stratification") +
labs(colour = "Stratification")
TempPrefMax_plot_weighted
## Warning: Removed 11 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 11 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 11 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 11 rows containing missing values (`geom_point()`).
# Two values with NA
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/TempPrefMax_plot_weighted.png", TempPrefMax_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 11 rows containing non-finite values (`stat_ydensity()`).
## Removed 11 rows containing missing values (`geom_point()`).
# TempPrefMax_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= TempPrefMax, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("TempPrefMax")
# TempPrefMax_plot
Weight_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= Weight, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,1000000)) +
ylab("Weight (g)") +
xlab("Stratification")
Weight_plot_weighted
## Warning: Removed 3 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 3 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 3 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 3 rows containing missing values (`geom_point()`).
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/Weight_plot_weighted.png", Weight_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 3 rows containing non-finite values (`stat_ydensity()`).
## Removed 3 rows containing missing values (`geom_point()`).
# Weight_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= Weight, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Weight")
# Weight_plot
CaudalFinLength_plot_weighted <- ggplot(Stratification_at_weighted, mapping = aes(x= Strat, y= CaudalFinLength, color = "black", fill = Strat)) +
geom_violin(alpha = 1, draw_quantiles = c(0.25, 0.5, 0.75)) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
geom_jitter(shape = 21,
size = 2,
alpha = 1,
width = 0.1) +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(-1,100)) +
ylab("Caudal Fin Length (cm)") +
xlab("Stratification")
CaudalFinLength_plot_weighted
## Warning: Removed 13 rows containing non-finite values (`stat_ydensity()`).
## Warning: Removed 13 rows containing missing values (`geom_point()`).
# Warning messages:
# 1: Removed 13 rows containing non-finite values (`stat_ydensity()`).
# 2: Removed 13 rows containing missing values (`geom_point()`).
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/CaudalFinLength_plot_weighted.png", CaudalFinLength_plot_weighted, width = 6, height = 4, units = "in")
## Warning: Removed 13 rows containing non-finite values (`stat_ydensity()`).
## Removed 13 rows containing missing values (`geom_point()`).
# CaudalFinLength_plot <- ggplot(Stratification_at, mapping = aes(x= Strat, y= CaudalFinLength, fill = Strat)) +
# geom_violin(alpha = 0.75, draw_quantiles = c(0.25, 0.5, 0.75)) +
# scale_fill_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# geom_jitter(shape = 21,
# size = 3,
# alpha = 0.75,
# width = 0.1) +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("CaudalFinLength")
# CaudalFinLength_plot
Stratification_at_props_FeedingPath <- Stratification_at %>%
group_by(Strat, FeedingPath) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
Stratification_at_props_FeedingPath <- na.omit(Stratification_at_props_FeedingPath)
FeedingPath_plot_weighted <- ggplot(Stratification_at_props_FeedingPath, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = FeedingPath)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = FeedingPath), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Diet Source", values = c(21:22), labels = c("b" = "benthic", "p" = "pelagic")) +
scale_color_viridis(alpha = 1, begin = 0.3, end = 0.85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = 0.85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,1)) +
ylab("Proportion") +
xlab("Stratification")
FeedingPath_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/FeedingPath_plot_weighted.png", FeedingPath_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# FeedingPath_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$FeedingPStratification_ath)
#
# # Divide each count by the total number of rows to find the proportion
# FeedingPath_props <- FeedingPath_counts/(rowSums(FeedingPath_counts))
# FeedingPath_props
#
# FeedingPath_props <- as.dStratification_ata.frame(FeedingPath_props)
#
# FeedingPath_props$Var1 <- factor(FeedingPath_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# FeedingPath_plot <- ggplot(FeedingPath_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Stratification")
# FeedingPath_plot
Stratification_at_props_RepGuild1 <- Stratification_at %>%
group_by(Strat, RepGuild1) %>%
summarise(count = sum(SiteSums)) %>%
group_by(Strat) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
Stratification_at_props_RepGuild1 <- na.omit(Stratification_at_props_RepGuild1)
RepGuild1_plot_weighted <- ggplot(Stratification_at_props_RepGuild1, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = RepGuild1)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = RepGuild1), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Egg Care", values = c(21:23), labels = c('2g' = 'guarders', '1b' = 'bearers', '3n' = 'nonguarders')) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,0.6)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "E")
RepGuild1_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/RepGuild1_plot_weighted.png", RepGuild1_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# RepGuild1_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$RepGuild1)
#
# # Divide each count by the total number of rows to find the proportion
# RepGuild1_props <- RepGuild1_counts/(rowSums(RepGuild1_counts))
# RepGuild1_props
#
# RepGuild1_props <- as.dStratification_ata.frame(RepGuild1_props)
#
# RepGuild1_props$Var1 <- factor(RepGuild1_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# RepGuild1_plot <- ggplot(RepGuild1_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Stratification")
# RepGuild1_plot
Stratification_at_props_RepGuild2 <- Stratification_at %>%
group_by(Strat, RepGuild2) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
Stratification_at_props_RepGuild2 <- na.omit(Stratification_at_props_RepGuild2)
RepGuild2_plot_weighted <- ggplot(Stratification_at_props_RepGuild2, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = RepGuild2)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = RepGuild2), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Egg Strategy", values = c(11, 21:25), labels = c('1ib' = 'live bearers', '6s' = 'egg scatterers', '3n' = 'nesters', '5h' = 'brood hiders', '4t' = 'clutch tenders', '2eb' = 'external brooders')) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,0.6)) +
ylab("Proportion") +
xlab("Stratification")
RepGuild2_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/RepGuild2_plot_weighted.png", RepGuild2_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# RepGuild2_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$RepGuild2)
#
# # Divide each count by the total number of rows to find the proportion
# RepGuild2_props <- RepGuild2_counts/(rowSums(RepGuild2_counts))
# RepGuild2_props
#
# RepGuild2_props <- as.dStratification_ata.frame(RepGuild2_props)
#
# RepGuild2_props$Var1 <- factor(RepGuild2_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# RepGuild2_plot <- ggplot(RepGuild2_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Stratification")
# RepGuild2_plot
Stratification_at_props_ParentalCare <- Stratification_at %>%
group_by(Strat, ParentalCare) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
Stratification_at_props_ParentalCare <- na.omit(Stratification_at_props_ParentalCare)
ParentalCare_plot_weighted <- ggplot(Stratification_at_props_ParentalCare, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = ParentalCare)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = ParentalCare), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Parental Care", values = c(21:25), labels = c('4n' = 'none', '3p' = 'paternal', '2m' = 'maternal', '1b' = 'biparental')) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,0.6)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "F")
ParentalCare_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/ParentalCare_plot_weighted.png", ParentalCare_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# ParentalCare_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$ParentalCare)
#
# # Divide each count by the total number of rows to find the proportion
# ParentalCare_props <- ParentalCare_counts/(rowSums(ParentalCare_counts))
# ParentalCare_props
#
# ParentalCare_props <- as.dStratification_ata.frame(ParentalCare_props)
#
# ParentalCare_props$Var1 <- factor(ParentalCare_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# ParentalCare_plot <- ggplot(ParentalCare_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Stratification")
# ParentalCare_plot
Fresh/Brack/Salt
Stratification_at_props_Water <- Stratification_at %>%
group_by(Strat, WaterPref) %>%
summarise(count = sum(SiteSums)) %>%
mutate(proportion = count/sum(count))
## `summarise()` has grouped output by 'Strat'. You can override using the
## `.groups` argument.
#Stratification_at_props_Water$Water <- factor(Stratification_at_props_Water$Water, levels = c("all", "fresh", "fresh-brack", "brack", "brack-salt", "salt"))
Water_plot_weighted <- ggplot(Stratification_at_props_Water, mapping = aes(x= Strat, y= proportion, color = "black", fill = Strat, shape = WaterPref)) +
geom_point(position = "identity", size = 6, aes(group = Strat)) +
geom_line(position = "identity", aes(group = WaterPref), linewidth = 0.5, linetype = "dotted") +
scale_shape_manual(name = "Water", values = c(21:23,11,24:25), labels = c('3a' = 'all', '1s' = 'salt', '2bs' = 'brack-salt', '4b' = 'brack', '5fb' = 'fresh-brack', '6f' = 'fresh')) +
scale_color_viridis(alpha = 1, begin = 0, end = .85, discrete = T, option = "G") +
scale_fill_viridis(alpha = 1, begin = 0.3, end = .85, discrete = T, option = "G") +
guides(fill = "none", color = "none") +
theme_bw() +
theme(text = element_text(size = 22), legend.text = element_text(size = 22),
axis.text = element_text(size = 22, color = "black"),
axis.line = element_line(color = "black"),
plot.background = element_blank(),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.border = element_blank()) +
ylim(c(0,1)) +
ylab("Proportion") +
xlab("Stratification") +
labs(colour = "Stratification", tag = "B")
Water_plot_weighted
ggsave("/Users/bailey/Documents/research/fish_biodiversity/figures/stratification_trait_plots/Water_plot_weighted.png", Water_plot_weighted, width = 6, height = 4, units = "in")
# # Identify how many individuals have one of the trait factors for each Stratification
# Habitat_counts <- table(Stratification_at$Stratification, row.names = Stratification_at$Habitat)
#
# # Divide each count by the total number of rows to find the proportion
# Habitat_props <- Habitat_counts/(rowSums(Habitat_counts))
# Habitat_props
#
# Habitat_props <- as.dStratification_ata.frame(Habitat_props)
#
# Habitat_props$Var1 <- factor(Habitat_props$Var1, levels = c("Reference", "Ocean", "Holomictic", "Meromictic"))
#
# Habitat_plot <- ggplot(Habitat_props, mapping = aes(x= Var1, y= Freq, color = Var1, shape = row.names)) +
# geom_point(position = "identity", size = 5, aes(group = Var1)) +
# scale_color_viridis(alpha = 0.5, end = 0.75, discrete = T, option = "G") +
# theme_bw() +
# theme(
# plot.background = element_blank(),
# panel.grid.major = element_blank(),
# panel.grid.minor = element_blank(),
# panel.border = element_blank(),
# axis.line = element_line(color = "black")) +
# ylab("Proportion") +
# xlab("Habitat")
# Habitat_plot
sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/Los_Angeles
## tzcode source: internal
##
## attached base packages:
## [1] parallel stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] tidyr_1.3.0 phytools_2.0-3 maps_3.4.1.1 ape_5.7-1
## [5] reshape2_1.4.4 stringr_1.5.1 knitr_1.45 viridis_0.6.4
## [9] viridisLite_0.4.2 ggplot2_3.4.4 dplyr_1.1.4
##
## loaded via a namespace (and not attached):
## [1] fastmatch_1.1-4 gtable_0.3.4 xfun_0.41
## [4] bslib_0.6.1 lattice_0.22-5 numDeriv_2016.8-1.1
## [7] quadprog_1.5-8 vctrs_0.6.5 tools_4.3.1
## [10] generics_0.1.3 tibble_3.2.1 fansi_1.0.6
## [13] highr_0.10 pkgconfig_2.0.3 Matrix_1.6-4
## [16] scatterplot3d_0.3-44 lifecycle_1.0.4 farver_2.1.1
## [19] compiler_4.3.1 textshaping_0.3.7 munsell_0.5.0
## [22] mnormt_2.1.1 combinat_0.0-8 codetools_0.2-19
## [25] htmltools_0.5.7 sass_0.4.8 yaml_2.3.7
## [28] pillar_1.9.0 jquerylib_0.1.4 MASS_7.3-60
## [31] cachem_1.0.8 clusterGeneration_1.3.8 iterators_1.0.14
## [34] foreach_1.5.2 nlme_3.1-164 phangorn_2.11.1
## [37] tidyselect_1.2.0 digest_0.6.33 stringi_1.8.2
## [40] purrr_1.0.2 labeling_0.4.3 fastmap_1.1.1
## [43] grid_4.3.1 colorspace_2.1-0 expm_0.999-8
## [46] cli_3.6.1 magrittr_2.0.3 optimParallel_1.0-2
## [49] utf8_1.2.4 withr_2.5.2 scales_1.3.0
## [52] rmarkdown_2.25 igraph_1.5.1 gridExtra_2.3
## [55] ragg_1.2.6 coda_0.19-4 evaluate_0.23
## [58] doParallel_1.0.17 rlang_1.1.2 Rcpp_1.0.11
## [61] glue_1.6.2 rstudioapi_0.15.0 jsonlite_1.8.8
## [64] R6_2.5.1 plyr_1.8.9 systemfonts_1.0.5